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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2023-04-03, 17:20 CEST based on data in:

        General Statistics

        Showing 370/370 rows and 4/6 columns.
        Sample Name% Dups% GCMedian Read LengthM Seqs
        SRR341616_1
        9.3%
        43%
        75 bp
        14.8
        SRR341616_2
        8.7%
        43%
        73 bp
        14.8
        SRR341617_1
        7.1%
        42%
        75 bp
        12.8
        SRR341617_2
        6.7%
        42%
        73 bp
        12.8
        SRR341618_1
        6.6%
        44%
        75 bp
        16.2
        SRR341618_2
        6.2%
        45%
        73 bp
        16.2
        SRR341619_1
        10.7%
        45%
        75 bp
        13.2
        SRR341619_2
        5.8%
        46%
        73 bp
        13.2
        SRR341620_1
        4.3%
        45%
        75 bp
        15.8
        SRR341620_2
        3.9%
        45%
        73 bp
        15.8
        SRR341621_1
        4.9%
        45%
        75 bp
        14.0
        SRR341621_2
        4.7%
        45%
        73 bp
        14.0
        SRR341622_1
        15.9%
        41%
        75 bp
        14.6
        SRR341622_2
        14.9%
        42%
        73 bp
        14.6
        SRR341623_1
        8.7%
        43%
        75 bp
        14.9
        SRR341623_2
        3.6%
        43%
        73 bp
        14.9
        SRR341624_1
        11.6%
        43%
        73 bp
        15.8
        SRR341624_2
        4.8%
        43%
        75 bp
        15.8
        SRR341625_1
        10.3%
        44%
        73 bp
        12.7
        SRR341625_2
        9.6%
        45%
        75 bp
        12.7
        SRR341626_1
        15.3%
        43%
        75 bp
        13.3
        SRR341626_2
        6.8%
        43%
        73 bp
        13.3
        SRR341627_1
        9.8%
        44%
        75 bp
        14.1
        SRR341627_2
        3.9%
        44%
        73 bp
        14.1
        SRR341628_1
        14.7%
        41%
        75 bp
        14.9
        SRR341628_2
        14.0%
        42%
        73 bp
        14.9
        SRR341629_1
        28.6%
        44%
        75 bp
        14.7
        SRR341629_2
        26.9%
        44%
        73 bp
        14.7
        SRR341630_1
        8.5%
        44%
        75 bp
        14.2
        SRR341630_2
        3.5%
        44%
        73 bp
        14.2
        SRR341631_1
        25.6%
        44%
        75 bp
        14.6
        SRR341631_2
        4.2%
        44%
        75 bp
        14.6
        SRR341632_1
        19.5%
        44%
        75 bp
        30.5
        SRR341632_2
        19.6%
        44%
        75 bp
        30.5
        SRR341633_1
        12.4%
        44%
        75 bp
        30.6
        SRR341633_2
        11.8%
        44%
        75 bp
        30.6
        SRR341634_1
        19.7%
        42%
        75 bp
        15.8
        SRR341634_2
        19.0%
        42%
        73 bp
        15.8
        SRR341635_1
        4.8%
        44%
        75 bp
        12.3
        SRR341635_2
        4.5%
        44%
        73 bp
        12.3
        SRR341636_1
        10.0%
        44%
        75 bp
        15.8
        SRR341636_2
        9.1%
        44%
        73 bp
        15.8
        SRR341637_1
        4.3%
        44%
        75 bp
        12.2
        SRR341637_2
        4.0%
        44%
        73 bp
        12.2
        SRR341638_1
        6.9%
        42%
        75 bp
        13.0
        SRR341638_2
        6.6%
        43%
        73 bp
        13.0
        SRR341639_1
        14.0%
        42%
        75 bp
        16.6
        SRR341639_2
        13.3%
        42%
        73 bp
        16.6
        SRR341640_1
        11.6%
        43%
        75 bp
        16.4
        SRR341640_2
        10.8%
        43%
        73 bp
        16.4
        SRR341641_1
        4.8%
        45%
        75 bp
        13.5
        SRR341641_2
        4.3%
        45%
        73 bp
        13.5
        SRR341642_1
        6.0%
        43%
        75 bp
        14.7
        SRR341642_2
        5.5%
        44%
        73 bp
        14.7
        SRR341643_1
        16.5%
        44%
        75 bp
        20.1
        SRR341643_2
        15.8%
        44%
        75 bp
        20.1
        SRR341644_1
        16.6%
        42%
        75 bp
        15.9
        SRR341644_2
        15.7%
        42%
        73 bp
        15.9
        SRR341645_1
        8.4%
        44%
        75 bp
        15.2
        SRR341645_2
        10.2%
        44%
        73 bp
        15.2
        SRR341646_1
        20.7%
        46%
        75 bp
        19.5
        SRR341646_2
        19.3%
        46%
        75 bp
        19.5
        SRR341647_1
        6.2%
        44%
        75 bp
        14.6
        SRR341647_2
        7.3%
        44%
        73 bp
        14.6
        SRR341648_1
        5.4%
        43%
        75 bp
        14.8
        SRR341648_2
        6.4%
        43%
        73 bp
        14.8
        SRR341649_1
        14.5%
        43%
        75 bp
        21.9
        SRR341649_2
        13.7%
        43%
        75 bp
        21.9
        SRR341650_1
        24.8%
        44%
        75 bp
        20.8
        SRR341650_2
        23.3%
        44%
        75 bp
        20.8
        SRR341651_1
        9.9%
        41%
        75 bp
        14.3
        SRR341651_2
        5.2%
        42%
        73 bp
        14.3
        SRR341652_1
        7.2%
        41%
        75 bp
        17.6
        SRR341652_2
        3.8%
        41%
        73 bp
        17.6
        SRR341653_1
        12.3%
        42%
        75 bp
        17.1
        SRR341653_2
        11.6%
        42%
        73 bp
        17.1
        SRR341690_1
        12.2%
        45%
        90 bp
        16.6
        SRR341690_2
        11.7%
        45%
        90 bp
        16.6
        SRR341691_1
        8.1%
        46%
        90 bp
        15.0
        SRR341691_2
        7.3%
        46%
        90 bp
        15.0
        SRR341692_1
        9.5%
        44%
        90 bp
        15.4
        SRR341692_2
        9.3%
        44%
        90 bp
        15.4
        SRR341693_1
        14.1%
        44%
        90 bp
        16.9
        SRR341693_2
        13.3%
        45%
        90 bp
        16.9
        SRR341694_1
        30.1%
        48%
        90 bp
        19.0
        SRR341694_2
        28.1%
        48%
        90 bp
        19.0
        SRR341695_1
        13.8%
        44%
        90 bp
        18.5
        SRR341695_2
        13.4%
        44%
        90 bp
        18.5
        SRR341696_1
        9.9%
        42%
        90 bp
        19.1
        SRR341696_2
        9.4%
        42%
        90 bp
        19.1
        SRR341697_1
        16.4%
        46%
        90 bp
        16.0
        SRR341697_2
        15.3%
        46%
        90 bp
        16.0
        SRR341698_1
        8.1%
        44%
        90 bp
        17.3
        SRR341698_2
        7.9%
        44%
        90 bp
        17.3
        SRR341699_1
        7.6%
        46%
        90 bp
        18.1
        SRR341699_2
        7.3%
        46%
        90 bp
        18.1
        SRR341700_1
        5.7%
        44%
        90 bp
        14.6
        SRR341700_2
        5.6%
        44%
        90 bp
        14.6
        SRR341701_1
        25.0%
        45%
        90 bp
        15.9
        SRR341701_2
        24.0%
        45%
        90 bp
        15.9
        SRR341702_1
        6.8%
        47%
        90 bp
        17.5
        SRR341702_2
        6.5%
        47%
        90 bp
        17.5
        SRR341703_1
        11.2%
        41%
        90 bp
        17.7
        SRR341703_2
        10.7%
        41%
        90 bp
        17.7
        SRR341704_1
        12.2%
        45%
        90 bp
        17.3
        SRR341704_2
        11.7%
        45%
        90 bp
        17.3
        SRR341705_1
        9.6%
        45%
        90 bp
        17.1
        SRR341705_2
        9.1%
        45%
        90 bp
        17.1
        SRR341706_1
        6.9%
        45%
        90 bp
        16.0
        SRR341706_2
        6.6%
        45%
        90 bp
        16.0
        SRR341707_1
        7.0%
        43%
        90 bp
        18.9
        SRR341707_2
        6.7%
        43%
        90 bp
        18.9
        SRR341708_1
        12.6%
        44%
        90 bp
        17.6
        SRR341708_2
        12.1%
        44%
        90 bp
        17.6
        SRR341709_1
        7.2%
        46%
        90 bp
        17.0
        SRR341709_2
        6.9%
        46%
        90 bp
        17.0
        SRR341710_1
        9.9%
        46%
        90 bp
        16.5
        SRR341710_2
        9.3%
        46%
        90 bp
        16.5
        SRR341711_1
        11.4%
        42%
        90 bp
        15.7
        SRR341711_2
        11.1%
        42%
        90 bp
        15.7
        SRR341712_1
        28.4%
        45%
        90 bp
        14.8
        SRR341712_2
        27.9%
        45%
        90 bp
        14.8
        SRR341713_1
        11.0%
        41%
        90 bp
        18.4
        SRR341713_2
        10.7%
        42%
        90 bp
        18.4
        SRR341714_1
        8.0%
        46%
        90 bp
        13.5
        SRR341714_2
        7.4%
        46%
        90 bp
        13.5
        SRR341715_1
        7.1%
        43%
        90 bp
        16.2
        SRR341715_2
        7.1%
        43%
        90 bp
        16.2
        SRR341716_1
        10.3%
        45%
        90 bp
        16.4
        SRR341716_2
        9.8%
        45%
        90 bp
        16.4
        SRR341717_1
        21.3%
        43%
        90 bp
        16.1
        SRR341717_2
        20.5%
        43%
        90 bp
        16.1
        SRR341718_1
        9.1%
        46%
        90 bp
        12.0
        SRR341718_2
        8.7%
        46%
        90 bp
        12.0
        SRR341719_1
        5.4%
        44%
        90 bp
        11.9
        SRR341719_2
        5.1%
        44%
        90 bp
        11.9
        SRR341720_1
        24.2%
        45%
        90 bp
        17.7
        SRR341720_2
        22.6%
        45%
        90 bp
        17.7
        SRR341721_1
        4.6%
        47%
        90 bp
        11.7
        SRR341721_2
        4.5%
        48%
        90 bp
        11.7
        SRR341722_1
        22.3%
        45%
        90 bp
        18.1
        SRR341722_2
        21.9%
        45%
        90 bp
        18.1
        SRR341723_1
        9.1%
        46%
        90 bp
        11.9
        SRR341723_2
        8.8%
        46%
        90 bp
        11.9
        SRR341724_1
        27.5%
        43%
        90 bp
        16.9
        SRR341724_2
        26.5%
        43%
        90 bp
        16.9
        SRR341725_1
        7.2%
        43%
        90 bp
        12.7
        SRR341725_2
        6.9%
        43%
        90 bp
        12.7
        SRR413556_1
        23.7%
        43%
        90 bp
        25.0
        SRR413556_2
        26.0%
        43%
        90 bp
        25.0
        SRR413557_1
        4.3%
        47%
        90 bp
        10.2
        SRR413557_2
        4.3%
        47%
        90 bp
        10.2
        SRR413558_1
        3.4%
        47%
        90 bp
        9.8
        SRR413558_2
        3.5%
        46%
        90 bp
        9.8
        SRR413559_1
        15.2%
        46%
        90 bp
        26.2
        SRR413559_2
        16.3%
        46%
        90 bp
        26.2
        SRR413560_1
        8.7%
        44%
        90 bp
        20.0
        SRR413560_2
        7.2%
        44%
        90 bp
        20.0
        SRR413561_1
        20.1%
        47%
        90 bp
        18.6
        SRR413561_2
        20.0%
        47%
        90 bp
        18.6
        SRR413562_1
        9.3%
        45%
        90 bp
        23.9
        SRR413562_2
        7.8%
        45%
        90 bp
        23.9
        SRR413563_1
        44.4%
        45%
        90 bp
        22.9
        SRR413563_2
        39.1%
        45%
        90 bp
        22.9
        SRR413564_1
        9.9%
        46%
        90 bp
        22.1
        SRR413564_2
        10.6%
        47%
        90 bp
        22.1
        SRR413565_1
        15.5%
        44%
        90 bp
        24.8
        SRR413565_2
        16.8%
        44%
        90 bp
        24.8
        SRR413566_1
        19.0%
        45%
        90 bp
        25.4
        SRR413566_2
        20.5%
        45%
        90 bp
        25.4
        SRR413575_1
        7.9%
        45%
        90 bp
        18.0
        SRR413575_2
        7.5%
        45%
        90 bp
        18.0
        SRR413576_1
        20.2%
        45%
        90 bp
        18.4
        SRR413576_2
        17.7%
        45%
        90 bp
        18.4
        SRR413577_1
        14.2%
        43%
        90 bp
        18.2
        SRR413577_2
        12.1%
        43%
        90 bp
        18.2
        SRR413578_1
        15.8%
        45%
        90 bp
        20.5
        SRR413578_2
        13.6%
        45%
        90 bp
        20.5
        SRR413579_1
        14.5%
        44%
        90 bp
        23.9
        SRR413579_2
        12.5%
        44%
        90 bp
        23.9
        SRR413580_1
        16.7%
        46%
        90 bp
        24.6
        SRR413580_2
        14.3%
        46%
        90 bp
        24.6
        SRR413581_1
        9.9%
        45%
        90 bp
        20.6
        SRR413581_2
        8.2%
        45%
        90 bp
        20.6
        SRR413582_1
        17.6%
        45%
        90 bp
        22.6
        SRR413582_2
        15.2%
        45%
        90 bp
        22.6
        SRR413583_1
        8.0%
        44%
        90 bp
        14.8
        SRR413583_2
        8.0%
        44%
        90 bp
        14.8
        SRR413584_1
        7.2%
        47%
        90 bp
        22.8
        SRR413584_2
        5.7%
        47%
        90 bp
        22.8
        SRR413585_1
        14.6%
        47%
        90 bp
        22.3
        SRR413585_2
        12.3%
        47%
        90 bp
        22.3
        SRR413586_1
        5.4%
        48%
        90 bp
        20.2
        SRR413586_2
        5.5%
        48%
        90 bp
        20.2
        SRR413587_1
        12.6%
        44%
        90 bp
        24.0
        SRR413587_2
        10.4%
        44%
        90 bp
        24.0
        SRR413588_1
        17.2%
        46%
        90 bp
        23.4
        SRR413588_2
        14.8%
        46%
        90 bp
        23.4
        SRR413589_1
        11.2%
        46%
        90 bp
        21.3
        SRR413589_2
        9.1%
        46%
        90 bp
        21.3
        SRR413590_1
        29.2%
        46%
        90 bp
        17.9
        SRR413590_2
        25.2%
        46%
        90 bp
        17.9
        SRR413592_1
        14.2%
        44%
        90 bp
        23.0
        SRR413592_2
        12.1%
        44%
        90 bp
        23.0
        SRR413593_1
        32.6%
        44%
        90 bp
        21.4
        SRR413593_2
        28.6%
        44%
        90 bp
        21.4
        SRR413594_1
        23.2%
        44%
        90 bp
        24.6
        SRR413594_2
        22.7%
        44%
        90 bp
        24.6
        SRR413595_1
        33.1%
        45%
        90 bp
        17.0
        SRR413595_2
        27.9%
        45%
        90 bp
        17.0
        SRR413596_1
        17.5%
        45%
        90 bp
        22.2
        SRR413596_2
        14.9%
        45%
        90 bp
        22.2
        SRR413597_1
        11.8%
        44%
        90 bp
        14.2
        SRR413597_2
        10.2%
        44%
        90 bp
        14.2
        SRR413598_1
        7.6%
        47%
        90 bp
        22.5
        SRR413598_2
        6.5%
        47%
        90 bp
        22.5
        SRR413599_1
        11.4%
        44%
        90 bp
        22.3
        SRR413599_2
        10.0%
        44%
        90 bp
        22.3
        SRR413600_1
        10.4%
        45%
        90 bp
        17.6
        SRR413600_2
        8.8%
        45%
        90 bp
        17.6
        SRR413601_1
        12.9%
        46%
        90 bp
        22.4
        SRR413601_2
        10.7%
        47%
        90 bp
        22.4
        SRR413602_1
        10.4%
        43%
        90 bp
        21.8
        SRR413602_2
        10.5%
        43%
        90 bp
        21.8
        SRR413603_1
        11.4%
        45%
        90 bp
        22.5
        SRR413603_2
        12.1%
        45%
        90 bp
        22.5
        SRR413604_1
        8.4%
        46%
        90 bp
        8.7
        SRR413604_2
        8.6%
        46%
        90 bp
        8.7
        SRR413605_1
        30.6%
        44%
        90 bp
        36.3
        SRR413605_2
        33.3%
        44%
        90 bp
        36.3
        SRR413606_1
        11.3%
        43%
        90 bp
        22.6
        SRR413606_2
        11.4%
        43%
        90 bp
        22.6
        SRR413607_1
        14.7%
        44%
        90 bp
        27.0
        SRR413607_2
        14.9%
        44%
        90 bp
        27.0
        SRR413608_1
        15.1%
        44%
        90 bp
        20.3
        SRR413608_2
        23.4%
        44%
        90 bp
        20.3
        SRR413609_1
        26.9%
        44%
        90 bp
        26.3
        SRR413609_2
        27.8%
        44%
        90 bp
        26.3
        SRR413610_1
        10.6%
        44%
        90 bp
        16.3
        SRR413610_2
        12.1%
        44%
        90 bp
        16.3
        SRR413611_1
        20.8%
        45%
        90 bp
        23.1
        SRR413611_2
        27.1%
        45%
        90 bp
        23.1
        SRR413612_1
        5.4%
        45%
        90 bp
        16.8
        SRR413612_2
        6.2%
        45%
        90 bp
        16.8
        SRR413613_1
        8.3%
        47%
        90 bp
        24.1
        SRR413613_2
        11.3%
        47%
        90 bp
        24.1
        SRR413614_1
        10.6%
        44%
        90 bp
        20.8
        SRR413614_2
        13.9%
        44%
        90 bp
        20.8
        SRR413615_1
        12.1%
        46%
        90 bp
        22.0
        SRR413615_2
        11.8%
        46%
        90 bp
        22.0
        SRR413616_1
        9.5%
        43%
        90 bp
        23.4
        SRR413616_2
        14.7%
        43%
        90 bp
        23.4
        SRR413617_1
        7.7%
        42%
        90 bp
        18.2
        SRR413617_2
        10.5%
        42%
        90 bp
        18.2
        SRR413618_1
        16.6%
        45%
        90 bp
        18.0
        SRR413618_2
        18.1%
        45%
        90 bp
        18.0
        SRR413619_1
        14.3%
        44%
        90 bp
        25.7
        SRR413619_2
        15.8%
        45%
        90 bp
        25.7
        SRR413620_1
        17.3%
        43%
        90 bp
        25.7
        SRR413620_2
        18.9%
        43%
        90 bp
        25.7
        SRR413621_1
        12.0%
        45%
        90 bp
        20.3
        SRR413621_2
        13.3%
        45%
        90 bp
        20.3
        SRR413622_1
        11.2%
        44%
        90 bp
        23.6
        SRR413622_2
        14.9%
        44%
        90 bp
        23.6
        SRR413623_1
        5.7%
        46%
        90 bp
        24.2
        SRR413623_2
        6.5%
        46%
        90 bp
        24.2
        SRR413624_1
        5.5%
        47%
        90 bp
        17.5
        SRR413624_2
        6.3%
        47%
        90 bp
        17.5
        SRR413625_1
        8.1%
        45%
        90 bp
        18.6
        SRR413625_2
        8.9%
        45%
        90 bp
        18.6
        SRR413626_1
        10.9%
        46%
        90 bp
        17.6
        SRR413626_2
        10.6%
        46%
        90 bp
        17.6
        SRR413627_1
        11.7%
        46%
        90 bp
        21.6
        SRR413627_2
        12.7%
        46%
        90 bp
        21.6
        SRR413628_1
        8.5%
        46%
        90 bp
        22.0
        SRR413628_2
        9.0%
        46%
        90 bp
        22.0
        SRR413629_1
        14.2%
        44%
        90 bp
        18.6
        SRR413629_2
        15.6%
        44%
        90 bp
        18.6
        SRR413630_1
        15.1%
        46%
        90 bp
        23.2
        SRR413630_2
        22.8%
        47%
        90 bp
        23.2
        SRR413631_1
        27.3%
        47%
        90 bp
        24.9
        SRR413631_2
        26.7%
        47%
        90 bp
        24.9
        SRR413632_1
        9.2%
        47%
        90 bp
        15.8
        SRR413632_2
        9.0%
        47%
        90 bp
        15.8
        SRR413633_1
        16.3%
        45%
        90 bp
        23.5
        SRR413633_2
        15.6%
        45%
        90 bp
        23.5
        SRR413634_1
        12.0%
        47%
        90 bp
        25.7
        SRR413634_2
        11.8%
        47%
        90 bp
        25.7
        SRR413635_1
        7.4%
        48%
        90 bp
        25.1
        SRR413635_2
        12.8%
        48%
        90 bp
        25.1
        SRR413636_1
        14.5%
        46%
        90 bp
        23.2
        SRR413636_2
        20.0%
        46%
        90 bp
        23.2
        SRR413637_1
        19.8%
        44%
        90 bp
        23.7
        SRR413637_2
        20.9%
        44%
        90 bp
        23.7
        SRR413638_1
        36.8%
        45%
        90 bp
        23.2
        SRR413638_2
        39.7%
        45%
        90 bp
        23.2
        SRR413639_1
        11.6%
        42%
        90 bp
        20.4
        SRR413639_2
        11.8%
        42%
        90 bp
        20.4
        SRR413640_1
        18.4%
        47%
        90 bp
        15.5
        SRR413640_2
        19.6%
        47%
        90 bp
        15.5
        SRR413641_1
        7.0%
        45%
        90 bp
        7.9
        SRR413641_2
        7.2%
        45%
        90 bp
        7.9
        SRR413642_1
        7.0%
        45%
        90 bp
        8.0
        SRR413642_2
        7.2%
        45%
        90 bp
        8.0
        SRR413643_1
        10.2%
        42%
        90 bp
        21.6
        SRR413643_2
        11.3%
        42%
        90 bp
        21.6
        SRR413644_1
        12.4%
        46%
        90 bp
        22.0
        SRR413644_2
        13.7%
        46%
        90 bp
        22.0
        SRR413645_1
        4.5%
        47%
        90 bp
        7.4
        SRR413645_2
        4.8%
        47%
        90 bp
        7.4
        SRR413646_1
        19.6%
        47%
        90 bp
        15.9
        SRR413646_2
        20.6%
        47%
        90 bp
        15.9
        SRR413647_1
        21.3%
        46%
        90 bp
        22.0
        SRR413647_2
        23.2%
        46%
        90 bp
        22.0
        SRR413648_1
        14.6%
        49%
        90 bp
        20.0
        SRR413648_2
        19.5%
        49%
        90 bp
        20.0
        SRR413649_1
        5.2%
        43%
        90 bp
        7.5
        SRR413649_2
        5.2%
        43%
        90 bp
        7.5
        SRR413650_1
        15.4%
        46%
        90 bp
        21.9
        SRR413650_2
        17.2%
        46%
        90 bp
        21.9
        SRR413651_1
        14.0%
        45%
        90 bp
        21.8
        SRR413651_2
        14.1%
        45%
        90 bp
        21.8
        SRR413652_1
        32.2%
        46%
        90 bp
        23.8
        SRR413652_2
        34.1%
        46%
        90 bp
        23.8
        SRR413653_1
        5.2%
        45%
        90 bp
        22.9
        SRR413653_2
        8.9%
        45%
        90 bp
        22.9
        SRR413654_1
        3.1%
        46%
        90 bp
        7.0
        SRR413654_2
        3.2%
        46%
        90 bp
        7.0
        SRR413655_1
        10.5%
        46%
        90 bp
        23.8
        SRR413655_2
        17.2%
        46%
        90 bp
        23.8
        SRR413656_1
        4.7%
        50%
        90 bp
        15.4
        SRR413656_2
        4.7%
        50%
        90 bp
        15.4
        SRR413657_1
        25.9%
        46%
        90 bp
        20.9
        SRR413657_2
        36.7%
        46%
        90 bp
        20.9
        SRR413658_1
        17.7%
        43%
        90 bp
        17.3
        SRR413658_2
        17.9%
        43%
        90 bp
        17.3
        SRR413659_1
        7.4%
        45%
        90 bp
        18.5
        SRR413659_2
        8.0%
        45%
        90 bp
        18.5
        SRR413660_1
        19.0%
        46%
        90 bp
        29.9
        SRR413660_2
        21.1%
        46%
        90 bp
        29.9
        SRR413661_1
        12.2%
        43%
        90 bp
        22.9
        SRR413661_2
        13.8%
        43%
        90 bp
        22.9
        SRR413662_1
        23.1%
        47%
        90 bp
        15.3
        SRR413662_2
        22.8%
        47%
        90 bp
        15.3
        SRR413663_1
        11.1%
        47%
        90 bp
        29.3
        SRR413663_2
        12.7%
        47%
        90 bp
        29.3
        SRR413664_1
        30.0%
        45%
        90 bp
        28.3
        SRR413664_2
        30.4%
        45%
        90 bp
        28.3
        SRR413665_1
        14.4%
        44%
        90 bp
        24.1
        SRR413665_2
        16.1%
        44%
        90 bp
        24.1
        SRR413666_1
        6.0%
        47%
        90 bp
        21.0
        SRR413666_2
        6.9%
        47%
        90 bp
        21.0
        SRR413667_1
        11.3%
        45%
        90 bp
        19.3
        SRR413667_2
        11.4%
        45%
        90 bp
        19.3
        SRR413668_1
        31.2%
        45%
        90 bp
        17.7
        SRR413668_2
        30.3%
        46%
        90 bp
        17.7
        SRR413669_1
        28.5%
        49%
        90 bp
        17.9
        SRR413669_2
        27.7%
        49%
        90 bp
        17.9
        SRR413670_1
        19.9%
        47%
        90 bp
        21.9
        SRR413670_2
        19.6%
        47%
        90 bp
        21.9
        SRR413671_1
        8.0%
        46%
        90 bp
        15.1
        SRR413671_2
        7.8%
        46%
        90 bp
        15.1
        SRR413672_1
        15.0%
        47%
        90 bp
        15.7
        SRR413672_2
        14.7%
        47%
        90 bp
        15.7
        SRR413688_1
        46.2%
        47%
        90 bp
        28.9
        SRR413688_2
        45.4%
        47%
        90 bp
        28.9
        SRR413758_1
        12.6%
        46%
        90 bp
        18.2
        SRR413758_2
        10.1%
        46%
        90 bp
        18.2
        SRR413768_1
        22.3%
        42%
        90 bp
        28.7
        SRR413768_2
        21.8%
        42%
        90 bp
        28.7

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        loading..

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        loading..

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        loading..

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        loading..

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        loading..

        Sequence Length Distribution

        All samples have sequences of a single length (73bp , 90bp , 75bp). See the General Statistics Table.

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

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        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        370 samples had less than 1% of reads made up of overrepresented sequences

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

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        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        loading..

        MultiQC v1.14 - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.